PCV boxplot per method (PRONE-style) — nm_plot

One boxplot per normalization method showing the per-protein CV distribution (CV averaged across groups for each protein). Lower and less spread values indicate better within-group consistency. With diff = TRUE, shows % reduction vs baseline as a bar chart.

Usage

nm_plot_pcv(
  se,
  assay_names = NULL,
  condition_col = "Condition",
  diff = FALSE,
  baseline = "log2",
  ...
)

Arguments

se: SummarizedExperiment from import_norm_matrices().
assay_names: Character vector of assay names to include. NULL = all.
condition_col: Column in colData with condition labels.
diff: Logical. If TRUE, show % reduction vs baseline. Default FALSE.
baseline: Character. Assay name used as reference for diff mode. Default "log2".
...: Additional arguments (unused).

Value

ggplot object.

Examples

data(nadia_dia)
se <- nm_prepare_se(nadia_dia, verbose = FALSE)
se <- nm_run_normalizations(se, methods = c("cycloess", "quantile", "MAD"),
                            verbose = FALSE)

nm_plot_pcv(se)


# Percent CV reduction relative to the unnormalized log2 baseline
nm_plot_pcv(se, diff = TRUE, baseline = "log2")